Antibodies have profound relevance as research tools and in diagnostic and therapeutic applications. However, the identification of such useful antibodies is difficult and frequently, especially if therapeutic applications are envisioned, requires considerable redesign or ‘humanization’ before the antibody is suitable for administration.
Previous methods for identifying desirable antibodies have typically involved phage display of representative antibodies, for example human libraries or synthetic libraries, however, these approaches have limitations. For example, most human libraries contain only the antibody sequence diversity that can be experimentally captured or cloned from the source tissue. Accordingly, the human library may lack or under represent other valuable antibody sequences. Synthetic or consensus libraries have other limitations such as the potential to encode non-naturally occurring sequence that has the potential to be immunogenic. In addition, synthetic libraries, in an effort to be comprehensive, frequently contain too much diversity and are difficult to screen. Moreover, these libraries, when used to identify a candidate antibody that binds to a particular target, are not amenable to rational, follow-up, affinity maturation techniques to improve the binding of the candidate molecule. For example, methods for subsequent antibody improvement often involve in vitro mutagenesis such as random mutagenesis, saturation mutagenesis, error-prone PCR, gene shuffling, and antibody chain shuffling. These strategies are inherently stochastic and often require the construction of exceedingly large libraries to explore any meaningful sequence diversity. As the number of positions to be mutated in a given antibody becomes larger, the size of the resultant library becomes larger than what can be feasibly screened.
A recently identified method has described in silico (and optionally in vitro) construction of universal antibody libraries that systematically represent non-immunogenic, naturally-occurring candidate antibodies that possess desired properties, e.g., libraries that are fully representative of known, prevalent (e.g., >10% frequency in a surveyed population), naturally-occurring CDR diversity in the germline (e.g., antibodies derived from the V BASE database) and/or in mature antibodies (e.g., antibodies derived from the Kabat database).
A need exists for a rational, efficient process by which the information regarding naturally-occurring sequence diversity that is contained within reference libraries, such as universal antibody libraries, may be optimally exploited to enhance antibody design (e.g., design of novel human antibodies possessing optimal affinity and minimal immunogenicity).